GEO series

Gene Expression Analysis of Stage I Endometrial Cancers

GSE17025 Homo sapiens (human) Expression microarray 103 samples Submitted 2011/12/13 Platform GPL570

At a glance

Expression microarray · human · 103 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Endometrial cancerThis series is part of our curated briefing on it.
Samples: 103 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Global gene expression patterns associated with early stage endometrial cancer have been reported, but changes in molecular expression associated with tumor grade, depth of myometrial invasion, and non-endometrioid histology have not been previously elucidated. Our group hypothesized there are unique genetic events underlying early endometrial carcinogenesis.

Read the full summary ↓

Ninety-two samples of pathologically reviewed stage I endometrial cancers (80 endometrioid and 12 serous) with a heterogeneous distribution of grade and depth of myometrial invasion (i.e. 9 IAG1, 14 IAG2, 7 IAG3, 14 IBG1, 12 IBG2, 13 IBG3, 7 ICG1, 10 ICG2, and 6 ICG3) were examined in relation to 12 samples of atrophic endometrium from postmenopausal women. Specimens were analyzed using oligonucleotide microarray analysis and a subset of the differentially expressed transcripts was validated using quantitative PCR. Comparison of early stage cancers with normal endometrium samples by the univariate t-test with 10,000 permutations identified 900 genes that were differentially regulated by at least 4-fold at a p value of <0.001. Unsupervised analysis revealed that when compared to normal endometrium, serous and endometrioid stage I cancers appeared to have similar expression patterns. However, when compared in the absence of normal controls, they were distinct. Differential expression analysis revealed a number of transcripts that were common as well as unique to both histologic types. This data uncovers previously unrecognized, novel pathways involved in early stage endometrial cancers and identifys targets for prevention strategies that are inclusive of both endometrioid and serous histologic subtypes.

This dataset

Open GSE17025 in finder → Find more human microarray datasets → Endometrial cancer landscape →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE17025_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA117807. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21619611) ↗

Samples in this study

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+ 103 more — browse all 103 samples with per-sample file links →

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GSE334100 Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [RNA-seq] 16 samples same disease briefing · shares endometrial
GSE278879 Single nucleus RNA sequencing analysis reveals transcriptional heterogeneity of endometrioid endometrial cancer 11 samples same disease briefing · shares endometrial
GSE298672 Altered gene expression by C1orf106 in endometrial cancer cells. 6 samples same disease briefing · shares endometrial
GSE272263 Adipocyte induced distinct gene expression profiling of human endometrioid endometrial cancer cells upon SIRT1 inhibition. 5 samples same disease briefing · shares endometrial
GSE307568 Patient-derived organoid – immune cell co-culture platform for therapeutics discovery in high-grade endometrial cancer 189 samples same disease briefing · shares endometrial
GSE312323 Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [SOX17_ChIPseq] 2 samples same disease briefing · shares endometrial

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